Biology 5A Homework 7 January 25-28, 2013

1.

We know from lecture that hydrophobic interaction is the clustering of nonpolar molecules or groups together in water to minimize disruption of H-bonding between water molecules. This homework problem will help you understand how clustering reduces the disruption of water H-bonding. Water molecules are in a lower energy configuration, and thus a more thermodynamically favorable situation, when they can form a maximum number of hydrogen bonds. When methyl groups are placed in water, the adjacent water molecules are restricted in the number of hydrogen bonds they can form, because methyl groups cannot form hydrogen bonds. This restriction means that there are fewer configurations of these adjacent waters that permit hydrogen bonding. In particular, these adjacent waters must be configured so they make hydrogen bonds only towards the surrounding water, away from the methyl groups. This restricted configuration of the adjacent water molecules means that they are more ordered than they would be if the methyl group was not there. Water molecules at the interface with the methyl group thus represent a thermodynamic dilemma: These interfacial water molecules would be in a lower energy configuration if they made more hydrogen bonds, but to make the most hydrogen bonds they must assume restricted configurations that are more ordered, which is not thermodynamically favorable. The larger the area of the interface between waters and methyl groups, the larger the amount of water that is limited in its hydrogen bonding, and the more unfavorable the situation. If something can happen to reduce the amount of interface, it will be spontaneous to do so. How much interface is there along which the hydrogen bonding of water to itself is limited? Consider a simplified two-dimensional model of what happens when four methyl groups are placed in water (See accompanying figure). Let us say that the methyl groups are squares of length L along each side. The perimeter, or total length of the water-methyl interface, around each methyl group is then L x 4. When the four methyl groups are spread out and separate in the water, as in the four corners of the figure, then the total length of the interface around the four methyl groups adds up to be (L 4) 4 = 16L. If the four methyl groups cluster together as shown in the center of the figure, however, then the cluster they form has a side of length 2L, and the perimeter, or total length of the water-methyl group interface around the cluster is 2L x 4 = 8L. Thus, the clustering of the four methyl groups in this simplified two-dimensional model reduces the water-methyl group interface from 16L to 8L, and this correspondingly reduces the amount of disruption of hydrogen bonding of water to itself. Problem: Extend this two-dimension model to three dimensions. Consider a cube of methyl groups that has a length L along each edge of the cube. The area of one

face of the cube is then L2, and the total area of the six faces of the cube is 6 x L2 = 6L2. Consider now eight such cubes, first spread out and separate, and then clustered together to make one large cube. How much water-methyl group interface is there when the eight cubes are separated, and how much water methyl group interface is there when the eight cubes are clustered together into one large cube? L H L H L HYDROPHOBIC INTERACTION H H H C C C L H H H TOTAL PERIMETER = 4L FOR EACH 4 X 4L = 16L

H C

2L H H C

H H H H

H H

TOTAL PERIMETER = 8L 2L

C H

H H

H C H A. B. C. D. E. (Ans. B)

H C

12L2 interface when separate, and 6L2 interface when clustered 48L2 interface when separate, and 24L2 interface when clustered 24L2 interface when separate, and 12L2 interface when clustered 48L2 interface when separate, and 36L2 interface when clustered 96L2 interface when separate, and 32L2 interface when clustered

2.

The accompanying figure shows a portion of a plasma membrane (the membrane at the outer border of the cell) containing three membrane proteins, I, II, and III. Protein I is considered a peripheral protein because it is associated with the surface of the membrane, but is not deeply embedded in the membrane. Proteins II and III are considered integral proteins because they are deeply embedded in the membrane. The letters A and B shown in protein III point to two locations on the surface of this protein. Which of the following statements is most likely to be true?

A.

B.

C. D. E. (Ans. B) 3.

Amino acid residues at location A are likely to have nonpolar side groups while amino acid residues at location B are likely to have polar side groups. Amino acid residues at location A are likely to have electrically charged side groups while amino acid residues at location B are likely to have nonpolar side groups. Amino acid residues at locations A and B are equally likely to have nonpolar side groups. Amino acid residues at locations A and B are equally likely to have polar side groups. Amino acid residues at locations A and B are equally likely to have electrically charged side groups.

The accompanying figure shows three views, I, II, and III, recorded at different times during a random walk (diffusion) experiment. Order these three views starting with the one that was recorded first and ending with the one that was recorded last. II < I < III I < II < III II < III < I III < I < II III < II < I

A. B. C. D. E. (Ans. D)

4.

During the development of grape fruits, the fruit cells take up large amounts of sucrose that is delivered to the fruit through the stem. This homework problem involves an experiment investigating the sucrose cotransport system that transports sucrose across the plasma membrane of fruit cells. In the experiment, the cell wall of developing fruit cells is enzymically digested away, and the resulting protoplasts (live plant cells with their cell wall removed) are allowed to settle down on a Teflon film that divides the upper and lower portions of a chamber filled with an aqueous medium. The Teflon film contains tiny (5 micrometer diameter) pores. The protoplasts settle over and adhere to the pores, and are then ruptured, leaving plasma membrane fragments spanning across the pores and acting as a semipermeable barrier between the upper and lower portions of the chamber (see one such membrane fragment, highly magnified, in the accompanying figure). The upper chamber corresponds to what was the inside of the cells, and the lower chamber corresponds to what was the outside of the cells. A voltmeter is connected between the solutions in the upper and lower chambers, and another electrode inserted into the upper chamber measures the pH there. After the system is set up, 5 mM ATP is added to the upper chamber at time T1 (see accompanying graph), which causes the reading on the voltmeter to gradually increase (dotted line in graph). At a later time T2, a valve is opened, allowing sucrose to enter the lower chamber and causing the voltage to decrease somewhat. Which of the solid lines in the graph shows the most likely time course of changes of the pH values in the upper chamber during this experiment?

A. B. C. D. E. (Ans. B)

curve A curve B curve C curve D curve E

5.

Suppose that you conduct some experiments with porcine (pig) red blood cells. You suspend samples of the cells in test media of various solutes and various solute concentrations. After several experiments, you realize that an error has been made in labeling at least one of the test media. Which of the following pairs of observations convinces you that something is wrong with the media? The cells lysed in 0.3 M glucose and crenated (shrunk) in 0.3 M NaCl. The cells lysed in 0.25 M CaCl2 and crenated (shrunk) in 0.3 M KCl. The cells lysed in 0.15 M NaCl and crenated (shrunk) in 0.6 M ribose. The cells lysed in 0.15 M KCl and crenated (shrunk) in 0.6 M glucose. The cells lysed in 0.3 M glucose and crenated (shrunk) in 0.6 M ribose.

A. B. C. D. E. (Ans. B)